If we're going based of canon, Silver's starter is a Totodile, but he has a Magmortar so that is just a slight change.
The story from Sero's perspective is really well flushed out, and I like the direction he's headed. It's quite obvious that he is driven by an intense hatred and a sense of ambition. Textbook bullied becomes the bully case. Making humanity linked to Pokemon evolution is also a clever touch as well.
But there is one thing that is bugging me, and that is this; what is Silver's motivation for all of this? If you remember (Heart)Gold and (Soul)Silver, there was nothing in existence that Silver detested more than Team Rocket. He saw Team Rocket as an extension of his father, whom he considered weak and a failure, and as such he projected that perception unto every single Team Rocket member. He ends up doing just as much damage to Team Rocket's operations as Gold does. Couple that with him opening himself up to his emotions and to his Pokemon at the end of the games, and I just don't see how he could possibly go down this path. On principle alone he would never associate himself with the brand of Team Rocket.
Sero doesn't seem like the kind of guy the new Silver would respect.either. The old Silver on the other hand...
Perhaps you should make their relationship a little more aged. What if the pact happened prior to the events of Gold and Silver? A young Sero and a young Silver are close friends growing up and create a pact to eventually become the two most powerful human beings in the Pokemon world.
After his father abandons him, Silver, who has now learned of Team Rocket's operations in Johto takes off to the Johto region with the intent of disbanding his father's branch of the organization once and for all, while becoming the world's strongest Pokemon trainer. (thus setting the events of gold and silver in motion) After learning about the importance of caring for your Pokemon and respecting your fellow trainers, Silver returns to his home region of Rakeo, where he discovers that not only is his old friend Sero is still driven by their old misguided philosophy, but he has made major headway into making their childhood dream come true.